Does the degradation in performance closely follow the spike in IOPS on the SQL Server?
I have a site that is using the same NetApp back end. We were having serious degradation at times, some of it seemed to line up with a spike in IOPS (nothing huge, maybe 3000 max) on a connected host, but most did not. It turned out the culprit was the relatively low amount of cache that NetApp put in the 3140 was being constantly flushed to disk because of some NAS shares on a totally different aggregate was being hammered.
My take away from that incident is to always get your storage vendor involved to take a look, even if you do not think the storage itself is the cause of the problem. A set of eyes from that end can not hurt, and may uncover an issue you did not realize you had.